BAC-end microsatellites from intra and inter-genic regions of the common bean genome and their correlation with cytogenetic features.

Matthew Wohlgemuth Blair,Deissy K Yuyó,Claritza Muñóz,Juana Marcela Córdoba,Jean-Marc Lacape

doi:10.1371/journal.pone.0101873

Abstract

Highly polymorphic markers such as simple sequence repeats (SSRs) or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES) from non-contigged, non-overlapping bacterial artificial clones (BACs) in common bean (Phaseolus vulgaris L.). These so called “singleton” BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally) and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.

Highlights

Grain legumes are part of a large plant family with special characteristic of symbiotic nitrogen fixation and high protein seeds [1]
Genome sequencing in common bean started with expressed sequence tags (ESTs) and bacterial artificial clones (BACs)-end sequences (BES) project and has progressed to a full shotgun sequence of the complete macromolecules representing each chromosome of G19833
BAC end sequencing projects are a rich source of sequences for marker development and for linking cytogenetic, genetic and physical maps

Summary

Introduction

Grain legumes are part of a large plant family with special characteristic of symbiotic nitrogen fixation and high protein seeds [1]. As a result, they are important for the human diet and for the nitrogen cycle of various agricultural systems. Phaseolus vulgaris L., common bean, is the grain legume with highest consumption around the world and plays an essential role in food security in the developing countries of Central America and Eastern or Southern Africa [2]. Common beans have many diverse landraces, modern cultivars and wild relatives within and outside the species limits of Phaseolus vulgaris [3]. Cultivars of common bean are especially diverse as many commercial classes exist for different grain types [2]

Methods

Results

Conclusion